* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/dsem.Rcheck’ * using R Under development (unstable) (2026-05-11 r90046) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 22.1.5 (https://github.com/llvm/llvm-project 5ea218a153f4d2f815b8244eab3e4b4ba5e00e6c) flang version 22.1.5 (https://github.com/llvm/llvm-project 5ea218a153f4d2f815b8244eab3e4b4ba5e00e6c) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-05-12 07:54:23 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘dsem/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dsem’ version ‘2.0.0’ * package encoding: UTF-8 * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘dsem’ can be installed ... [541s/558s] OK * used C++ compiler: ‘clang version 22.1.5 (https://github.com/llvm/llvm-project 5ea218a153f4d2f815b8244eab3e4b4ba5e00e6c)’ * checking package directory ... OK * checking whether the package can be loaded ... [30s/30s] OK * checking whether the package can be loaded with stated dependencies ... [23s/24s] OK * checking whether the package can be unloaded cleanly ... [22s/22s] OK * checking whether the namespace can be loaded with stated dependencies ... [25s/25s] OK * checking whether the namespace can be unloaded cleanly ... [28s/29s] OK * checking loading without being on the library search path ... [29s/29s] OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [77s/78s] OK * checking tests ... [404s/410s] ERROR Running ‘testthat.R’ [403s/409s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > > > library(testthat) > library(dsem) > > # Run tests > testthat::test_check("dsem") Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 mu_j 2 Random 3 x_tj 200 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 7 Fixed 2 delta0_j 2 Fixed 3 lnsigma_j 2 Fixed 4 mu_j 2 Random 5 x_tj 122 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 7 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random 4 x_tj 122 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 7 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random 4 x_tj 122 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 7 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 7 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random Read 5 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 6 Fixed 2 delta0_j 2 Fixed 3 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 4 Fixed 2 mu_j 2 Fixed Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 4 Fixed 2 mu_j 2 Fixed 3 x_tj 100 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 4 Fixed 2 mu_j 2 Fixed 3 x_tj 100 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 4 Fixed 2 mu_j 2 Fixed 3 x_tj 100 Random Read 10 records Coefficient_name Number_of_coefficients Type 1 beta_z 17 Fixed 2 mu_j 8 Random $par beta_z beta_z beta_z beta_z beta_z beta_z 0.28417790 -0.03841437 0.84012277 0.44333141 0.36664513 -0.12270679 beta_z beta_z beta_z beta_z beta_z beta_z 0.43580399 0.15036987 0.12793940 6.49358658 10.80899505 0.69515907 beta_z beta_z beta_z beta_z beta_z 4.21165242 1.34847427 2.00838610 0.92424304 10.61133205 $objective [1] 431.6122 attr(,"logarithm") [1] TRUE $convergence [1] 0 $iterations [1] 80 $evaluations function gradient 94 81 $message [1] "relative convergence (4)" Read 10 records Coefficient_name Number_of_coefficients Type 1 beta_z 17 Fixed 2 mu_j 8 Random Read 10 records Coefficient_name Number_of_coefficients Type 1 beta_z 17 Fixed 2 mu_j 8 Random Read 10 records Coefficient_name Number_of_coefficients Type 1 beta_z 17 Fixed 2 lnsigma_j 2 Fixed 3 mu_j 8 Random 4 x_tj 44 Random Read 3 items Read 10 records Coefficient_name Number_of_coefficients Type 1 beta_z 17 Fixed 2 mu_j 8 Random Read 0 records Coefficient_name Number_of_coefficients Type 1 beta_z 2 Fixed 2 mu_j 2 Random Read 2 records Coefficient_name Number_of_coefficients Type 1 beta_z 2 Fixed 2 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 4 Fixed 2 mu_j 2 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 lnsigma_j 2 Fixed 2 mu_j 2 Random 3 x_tj 122 Random Read 16 records Coefficient_name Number_of_coefficients Type 1 beta_z 24 Fixed 2 mu_j 8 Fixed 3 x_tj 232 Random Read 4 records Coefficient_name Number_of_coefficients Type 1 beta_z 5 Fixed 2 mu_j 4 Random Read 14 items Read 16 records Coefficient_name Number_of_coefficients Type 1 beta_z 24 Fixed 2 mu_j 8 Fixed 3 x_tj 232 Random ================================================================= ==1998427==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7d9892b3b170 at pc 0x7bc8788f4a16 bp 0x7ffd3f784510 sp 0x7ffd3f784508 READ of size 4 at 0x7d9892b3b170 thread T0 #0 0x7bc8788f4a15 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13 #1 0x7bc8782e5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #2 0x5647ad761f76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #3 0x5647ad76f785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #4 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #5 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #6 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #7 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #8 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #9 0x5647ad81426e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #10 0x5647ad811bd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #11 0x5647ad86aa75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #12 0x5647ad8116f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #13 0x5647ad868119 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #14 0x5647ad8116f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #15 0x5647ad86f503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #16 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #17 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #18 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #19 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #20 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #21 0x5647ad81426e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #22 0x5647ad811bd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #23 0x5647ad86fe6a in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #24 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #25 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #26 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #27 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #28 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #29 0x5647ad8625f4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #30 0x5647ad8625f4 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2465:8 #31 0x5647ad619d11 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #32 0x5647ad919369 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #33 0x5647ad824e43 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #34 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #35 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #36 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #37 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #38 0x5647ad81426e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #39 0x5647ad811bd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #40 0x5647ad8e2a91 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #41 0x5647ad8e52c0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #42 0x5647ad8e52c0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #43 0x5647ad8e5352 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #44 0x5647ad5e6d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #45 0x7fc894612574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #46 0x7fc894612627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #47 0x5647ad4fe7d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d9892b3b170 is located 0 bytes after 2288-byte region [0x7d9892b3a880,0x7d9892b3b170) allocated by thread T0 here: #0 0x5647ad5a3bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7bc878512fe6 in Eigen::internal::handmade_aligned_malloc(unsigned long, unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:105:20 #2 0x7bc878512fe6 in Eigen::internal::aligned_malloc(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:188:14 #3 0x7bc878512fe6 in void* Eigen::internal::conditional_aligned_malloc(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:241:10 #4 0x7bc878512fe6 in int* Eigen::internal::conditional_aligned_new_auto(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:404:36 #5 0x7bc878512fe6 in Eigen::DenseStorage::resize(long, long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639:20 #6 0x7bc87877c899 in Eigen::PlainObjectBase>::resize(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285:19 #7 0x7bc87877c899 in void Eigen::internal::resize_if_allowed, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, int, int>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764:9 #8 0x7bc87877c899 in void Eigen::internal::call_dense_assignment_loop, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778:3 #9 0x7bc87877c899 in Eigen::internal::Assignment, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #10 0x7bc87877c899 in void Eigen::internal::call_assignment_no_alias, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #11 0x7bc87877c899 in Eigen::Array& Eigen::PlainObjectBase>::_set_noalias, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:7 #12 0x7bc87877c899 in void Eigen::PlainObjectBase>::_init1, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:883:13 #13 0x7bc87877c899 in Eigen::Array::Array, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Array.h:210:22 #14 0x7bc87877c899 in tmbutils::vector::vector, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>) /data/gannet/ripley/R/test-clang/TMB/include/tmbutils/vector.hpp:24:16 #15 0x7bc87877c899 in tmbutils::vector asVector(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:114:21 #16 0x7bc8788c51e6 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:413:5 #17 0x7bc8782e5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #18 0x5647ad761f76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #19 0x5647ad76f785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #20 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #21 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #22 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #23 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #24 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #25 0x5647ad81426e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #26 0x5647ad811bd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #27 0x5647ad86aa75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #28 0x5647ad8116f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #29 0x5647ad868119 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #30 0x5647ad8116f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #31 0x5647ad86f503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #32 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #33 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #34 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #35 0x5647ad85994c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #36 0x5647ad858b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #37 0x5647ad81426e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #38 0x5647ad811bd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #39 0x5647ad86fe6a in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #40 0x5647ad81f62a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #41 0x5647ad812c24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #42 0x5647ad8111b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13 in objective_function::operator()() Shadow bytes around the buggy address: 0x7d9892b3ae80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3af00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3af80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3b000: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3b080: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7d9892b3b100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00[fa]fa 0x7d9892b3b180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d9892b3b200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d9892b3b280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3b300: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d9892b3b380: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==1998427==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [449s/458s] ERROR Error(s) in re-building vignettes: --- re-building ‘features.Rmd’ using rmarkdown Read 3 items Read 4 records --- finished re-building ‘features.Rmd’ --- re-building ‘model-description.Rmd’ using rmarkdown --- finished re-building ‘model-description.Rmd’ --- re-building ‘nonlinear.Rmd’ using rmarkdown ================================================================= ==2210552==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7d6b94fc7570 at pc 0x7b9b7b0f4a16 bp 0x7ffebec83a70 sp 0x7ffebec83a68 READ of size 4 at 0x7d6b94fc7570 thread T0 #0 0x7b9b7b0f4a15 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13 #1 0x7b9b7aae5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #2 0x55ed9121af76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #3 0x55ed91228785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #4 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #5 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #6 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #7 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #8 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #9 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #10 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #11 0x55ed91323a75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #12 0x55ed912ca6f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #13 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #14 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #15 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #16 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #17 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #18 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #19 0x55ed91329733 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #20 0x55ed913d2369 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #21 0x55ed912dde43 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #22 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #23 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #24 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #25 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #26 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #27 0x55ed912f7061 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6 #28 0x55ed912f7061 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20 #29 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #30 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #31 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #32 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #33 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #34 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #35 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #36 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #37 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #38 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #39 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #40 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #41 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #42 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #43 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #44 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #45 0x55ed912ebd6a in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #46 0x55ed912ebd6a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8121:16 #47 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #48 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #49 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #50 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #51 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #52 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #53 0x55ed9139ba91 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #54 0x55ed9139e2c0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #55 0x55ed9139e2c0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #56 0x55ed9139e352 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #57 0x55ed9109fd3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #58 0x7f9b98311574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x7f9b98311627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #60 0x55ed90fb77d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7d6b94fc7570 is located 0 bytes after 2288-byte region [0x7d6b94fc6c80,0x7d6b94fc7570) allocated by thread T0 here: #0 0x55ed9105cbb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7b9b7ad12fe6 in Eigen::internal::handmade_aligned_malloc(unsigned long, unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:105:20 #2 0x7b9b7ad12fe6 in Eigen::internal::aligned_malloc(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:188:14 #3 0x7b9b7ad12fe6 in void* Eigen::internal::conditional_aligned_malloc(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:241:10 #4 0x7b9b7ad12fe6 in int* Eigen::internal::conditional_aligned_new_auto(unsigned long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/util/Memory.h:404:36 #5 0x7b9b7ad12fe6 in Eigen::DenseStorage::resize(long, long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639:20 #6 0x7b9b7af7c899 in Eigen::PlainObjectBase>::resize(long, long) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285:19 #7 0x7b9b7af7c899 in void Eigen::internal::resize_if_allowed, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, int, int>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764:9 #8 0x7b9b7af7c899 in void Eigen::internal::call_dense_assignment_loop, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778:3 #9 0x7b9b7af7c899 in Eigen::internal::Assignment, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op, Eigen::internal::Dense2Dense, void>::run(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:5 #10 0x7b9b7af7c899 in void Eigen::internal::call_assignment_no_alias, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::internal::assign_op>(Eigen::Array&, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&, Eigen::internal::assign_op const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:3 #11 0x7b9b7af7c899 in Eigen::Array& Eigen::PlainObjectBase>::_set_noalias, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:7 #12 0x7b9b7af7c899 in void Eigen::PlainObjectBase>::_init1, Eigen::Map, 0, Eigen::Stride<0, 0>> const>, Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::DenseBase, Eigen::Map, 0, Eigen::Stride<0, 0>> const>> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:883:13 #13 0x7b9b7af7c899 in Eigen::Array::Array, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const> const&) /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/Core/Array.h:210:22 #14 0x7b9b7af7c899 in tmbutils::vector::vector, Eigen::Map, 0, Eigen::Stride<0, 0>> const>>(Eigen::CwiseUnaryOp, Eigen::Map, 0, Eigen::Stride<0, 0>> const>) /data/gannet/ripley/R/test-clang/TMB/include/tmbutils/vector.hpp:24:16 #15 0x7b9b7af7c899 in tmbutils::vector asVector(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:114:21 #16 0x7b9b7b0c51e6 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:413:5 #17 0x7b9b7aae5b91 in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #18 0x55ed9121af76 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #19 0x55ed91228785 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #20 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #21 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #22 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #23 0x55ed9131294c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #24 0x55ed91311b08 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #25 0x55ed912cd26e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #26 0x55ed912cabd8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #27 0x55ed91323a75 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #28 0x55ed912ca6f0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #29 0x55ed91328503 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #30 0x55ed912d862a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #31 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #32 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #33 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #34 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #35 0x55ed91329733 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4018:9 #36 0x55ed913d2369 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #37 0x55ed912dde43 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #38 0x55ed912cbc24 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #39 0x55ed912ca1b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #40 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #41 0x55ed912ca3a5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1185:6 #42 0x55ed912cc4ba in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/dsem/src/dsem.cpp:453:13 in objective_function::operator()() Shadow bytes around the buggy address: 0x7d6b94fc7280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7300: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7380: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7d6b94fc7500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00[fa]fa 0x7d6b94fc7580: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6b94fc7600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d6b94fc7680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7d6b94fc7780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==2210552==ABORTING --- re-building ‘random_slopes.Rmd’ using rmarkdown --- finished re-building ‘random_slopes.Rmd’ --- re-building ‘spatial_diffusion.Rmd’ using rmarkdown Read 21 records --- finished re-building ‘spatial_diffusion.Rmd’ SUMMARY: processing the following file failed: ‘nonlinear.Rmd’ Error: Vignette re-building failed. Execution halted * DONE Status: 2 ERRORs